{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T01:47:23Z","timestamp":1789004843435,"version":"build-2803163510"},"reference-count":138,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2023,11,20]],"date-time":"2023-11-20T00:00:00Z","timestamp":1700438400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006507","name":"Inova FIOCRUZ","doi-asserted-by":"publisher","award":["FIO-0167-00015.01.00\/20"],"award-info":[{"award-number":["FIO-0167-00015.01.00\/20"]}],"id":[{"id":"10.13039\/501100006507","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Oswaldo Cruz Foundation","award":["FIO-0167-00015.01.00\/20"],"award-info":[{"award-number":["FIO-0167-00015.01.00\/20"]}]},{"name":"Foundation to Support Scientific and Technological Development of Cear\u00e1\u2014FUNCAP\/Brazil","award":["FIO-0167-00015.01.00\/20"],"award-info":[{"award-number":["FIO-0167-00015.01.00\/20"]}]},{"name":"the Brazilian National Council for Scientific and Technological Development.\u2014CNPq\/Brazil","award":["FIO-0167-00015.01.00\/20"],"award-info":[{"award-number":["FIO-0167-00015.01.00\/20"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>The COVID-19 disease, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), emerged in late 2019 and rapidly spread worldwide, becoming a pandemic that infected millions of people and caused significant deaths. COVID-19 continues to be a major threat, and there is a need to deepen our understanding of the virus and its mechanisms of infection. To study the cellular responses to SARS-CoV-2 infection, we performed an RNA sequencing of infected vs. uninfected Calu-3 cells. Total RNA was extracted from infected (0.5 MOI) and control Calu-3 cells and converted to cDNA. Sequencing was performed, and the obtained reads were quality-analyzed and pre-processed. Differential expression was assessed with the EdgeR package, and functional enrichment was performed in EnrichR for Gene Ontology, KEGG pathways, and WikiPathways. A total of 1040 differentially expressed genes were found in infected vs. uninfected Calu-3 cells, of which 695 were up-regulated and 345 were down-regulated. Functional enrichment analyses revealed the predominant up-regulation of genes related to innate immune response, response to virus, inflammation, cell proliferation, and apoptosis. These transcriptional changes following SARS-CoV-2 infection may reflect a cellular response to the infection and help to elucidate COVID-19 pathogenesis, in addition to revealing potential biomarkers and drug targets.<\/jats:p>","DOI":"10.3390\/pathogens12111373","type":"journal-article","created":{"date-parts":[[2023,11,20]],"date-time":"2023-11-20T10:32:32Z","timestamp":1700476352000},"page":"1373","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Transcriptional Profiling of SARS-CoV-2-Infected Calu-3 Cells Reveals Immune-Related Signaling Pathways"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0331-414X","authenticated-orcid":false,"given":"Eric Petterson Viana","family":"Pereira","sequence":"first","affiliation":[{"name":"Superior Institute of Biomedical Sciences, State University of Cear\u00e1, Fortaleza 60714-903, CE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stela Mirla","family":"da Silva Felipe","sequence":"additional","affiliation":[{"name":"Superior Institute of Biomedical Sciences, State University of Cear\u00e1, Fortaleza 60714-903, CE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raquel Martins","family":"de Freitas","sequence":"additional","affiliation":[{"name":"Superior Institute of Biomedical Sciences, State University of Cear\u00e1, Fortaleza 60714-903, CE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0660-0459","authenticated-orcid":false,"given":"Jos\u00e9 Edn\u00e9sio","family":"da Cruz Freire","sequence":"additional","affiliation":[{"name":"Superior Institute of Biomedical Sciences, State University of Cear\u00e1, Fortaleza 60714-903, CE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio Edson Rocha","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Experimental Biology Center, University of Fortaleza, Fortaleza 60811-905, CE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nat\u00e1lia","family":"Canabrava","sequence":"additional","affiliation":[{"name":"Biotechnology and Molecular Biology Laboratory, State University of Cear\u00e1, Fortaleza 60714-903, CE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3592-4444","authenticated-orcid":false,"given":"Paula Matias","family":"Soares","sequence":"additional","affiliation":[{"name":"Superior Institute of Biomedical Sciences, State University of Cear\u00e1, Fortaleza 60714-903, CE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5819-0861","authenticated-orcid":false,"given":"Mauricio Fraga","family":"van Tilburg","sequence":"additional","affiliation":[{"name":"Biotechnology and Molecular Biology Laboratory, State University of Cear\u00e1, Fortaleza 60714-903, CE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Izabel Florindo","family":"Guedes","sequence":"additional","affiliation":[{"name":"Biotechnology and Molecular Biology Laboratory, State University of Cear\u00e1, Fortaleza 60714-903, CE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8950-742X","authenticated-orcid":false,"given":"Chad Eric","family":"Grueter","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4839-4400","authenticated-orcid":false,"given":"V\u00e2nia Marilande","family":"Ceccatto","sequence":"additional","affiliation":[{"name":"Superior Institute of Biomedical Sciences, State University of Cear\u00e1, Fortaleza 60714-903, CE, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,11,20]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (2023, August 24). 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